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Abstract

Amino acids are important organic compounds used as the fundamental building blocks of proteins: the extensive toolkit of the cell. Amino acids encode three-dimensional structure to define stability, folding, activity, and function of proteins. Our focus is the two-helix bundle needle proteins in the pathogenic bacterium Shigella flexneri. Type 3 secretion systems in gram-negative bacteria species cause the following diseases: typhoid fever, food poisoning, and gastroenteritis. This folding code introduces structural biases into an amino acid sequence, which defines the final protein structure. Synonymous research conducted begins with a stable fold and varying sequence to determine sequence diversity for a fold, while our method is the opposite. We composed a simple amino acid sequence mainly of alanine (polyAK), which is known to form alpha-helical secondary structure but has no long range contacts. This model peptide was altered by introduction of four more amino acids known to shape the peptide into a turn taken from the needle protein (PSDP). This sequence should create a two-helix bundle protein with long range contacts in silico. We use Monte Carlo computational simulations which determine favorable structures from given sequence to investigate peptide diversity. We probed our peptides over the temperature range 280 to 460 K. The results showed a transition from a compact globule to an expanded coil with increasing temperature for both peptides. The radius of gyration was used to examine compactness. Helical structure was also reviewed. Our results show the compact globule is significantly stabilized by PSDP addition. The polyAK peptide is more expanded at higher temperatures than the PSDP peptide. Thus, a turn can bias the conformation of polypeptides to a compact, globular structure. Future work will include laboratory investigations featuring these model peptides. Knowledge gained will be applied to understand the folding code in type 3 secretion systems.

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Apr 12th, 3:00 PMApr 12th, 4:00 PM

Questioning the Role of Turn Sequences within the Protein Folding Code

UC Ballroom

Amino acids are important organic compounds used as the fundamental building blocks of proteins: the extensive toolkit of the cell. Amino acids encode three-dimensional structure to define stability, folding, activity, and function of proteins. Our focus is the two-helix bundle needle proteins in the pathogenic bacterium Shigella flexneri. Type 3 secretion systems in gram-negative bacteria species cause the following diseases: typhoid fever, food poisoning, and gastroenteritis. This folding code introduces structural biases into an amino acid sequence, which defines the final protein structure. Synonymous research conducted begins with a stable fold and varying sequence to determine sequence diversity for a fold, while our method is the opposite. We composed a simple amino acid sequence mainly of alanine (polyAK), which is known to form alpha-helical secondary structure but has no long range contacts. This model peptide was altered by introduction of four more amino acids known to shape the peptide into a turn taken from the needle protein (PSDP). This sequence should create a two-helix bundle protein with long range contacts in silico. We use Monte Carlo computational simulations which determine favorable structures from given sequence to investigate peptide diversity. We probed our peptides over the temperature range 280 to 460 K. The results showed a transition from a compact globule to an expanded coil with increasing temperature for both peptides. The radius of gyration was used to examine compactness. Helical structure was also reviewed. Our results show the compact globule is significantly stabilized by PSDP addition. The polyAK peptide is more expanded at higher temperatures than the PSDP peptide. Thus, a turn can bias the conformation of polypeptides to a compact, globular structure. Future work will include laboratory investigations featuring these model peptides. Knowledge gained will be applied to understand the folding code in type 3 secretion systems.